Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Sequential Windowed Acquisition of Reporter Masses for Quantitation-First Proteomics

ABSTRACT: Initial SWARM datasets generated for feasibility testing of the SWARM+PRM methodology. These explorations touch upon a novel paradigm for acquisition of isobaric tagged proteomics data by mass spectrometry, and places relative quantitation ahead of identification. In this way, fragmentation and identification decisions can be predicated upon the quantitative trends of the analyte.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Escherichia Coli (ncbitaxon:562) Homo Sapiens (ncbitaxon:9606)

SUBMITTER: James A. Wohlschlegel

PROVIDER: MSV000083088 | MassIVE | Wed Oct 31 17:06:00 GMT 2018

SECONDARY ACCESSION(S): PXD011544

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Sequential Windowed Acquisition of Reporter Masses for Quantitation-First Proteomics.

Project description:The standard approach for proteomic data acquisition of isobaric-tagged samples by mass spectrometry is data-dependent acquisition. This semistochastic, identification-first paradigm generates a wealth of peptide-level data without regard to relative abundance. We introduce a data acquisition concept called sequential windowed acquisition of reporter masses (SWARM). This approach performs quantitation first, thereby allowing subsequent acquisition decisions to be predicated on user-defined patterns of reporter ion intensities. The efficacy of this approach is validated through experiments with both synthetic mixtures of Escherichia coli ribosomes spiked into human cell lysates at known ratios and the quantitative evaluation of the human proteome's response to the inhibition of cullin-based protein ubiquitination via the small molecule MLN4924. We find that SWARM-informed parallel reaction monitoring acquisitions display effective acquisition biasing toward analytes displaying quantitative characteristics of interest, resulting in an improvement in the detection of differentially abundant analytes. The SWARM concept provides a flexible platform for the further development of new acquisition methods.

| S-EPMC6859794 | biostudies-literature

Project description:An in tandem multiilocus mosquito identification methodology

| PRJNA681030 | ENA

Project description:An in tandem multiilocus Culicoides identification methodology

| PRJNA748077 | ENA

Sequential Labeling for Protein Quantitation, Raijmakers et al.

Project description:Not available

2008-02-29 | PRD000045 | Pride

Automated online sequential isotope labeling for protein quantitation applied to proteasome tissue-specific diversity.

Project description:Quantitation of protein abundance is a vital component in the proteomic analysis of biological systems, which can be achieved by differential stable isotopic labeling. To analyze tissue-derived samples, the isotopic labeling can be performed using chemical labeling of the peptides post-digestion. Standard chemical labeling procedures often require many manual sample handling steps, reducing the accuracy of measurements. Here, we describe a fully automated, online (in nanoLC columns), labeling procedure, which allows protein quantitation using differential isotopic dimethyl labeling of peptide N termini and lysine residues. We show that the method allows reliable quantitation over a wide dynamic range and can be used to quantify differential protein abundances in lysates and, more targeted, differences in composition between purified protein complexes. We apply the method to determine the differences in composition between bovine liver and spleen 20 S core proteasome complexes. We find that although all catalytically active immunoproteasome subunits were up-regulated in spleen (compared with liver), only one of the normal catalytic subunits was down-regulated, suggesting that the tissue-specific immunoproteasome assembly is more diverse than previously assumed.

| S-EPMC2556017 | biostudies-other

Plasma Cell-free RNA Signatures of Inflammatory Syndromes in Children

Project description:Inflammatory syndromes, including those caused by infection, are a major cause of hospital admissions among children and are often misdiagnosed because of a lack of advanced molecular diagnostic tools. In this study, we explored the utility of circulating cell-free RNA (cfRNA) in plasma as an analyte for the differential diagnosis and characterization of pediatric inflammatory syndromes. We profiled cfRNA in 370 plasma samples from pediatric patients with a range of inflammatory conditions, including Kawasaki disease (KD), Multisystem Inflammatory Syndrome in Children (MIS-C), viral infections and bacterial infections. We developed machine learning models based on these cfRNA profiles, which effectively differentiated KD from MIS-C — two conditions presenting with overlapping symptoms — with high performance (Test Area Under the Curve (AUC) = 0.97). We further extended this methodology into a multiclass machine learning framework that achieved 81% accuracy in distinguishing among KD, MIS-C, viral, and bacterial infections. We further demonstrated that cfRNA profiles can be used to quantify injury to specific tissues and organs, including the liver, heart, endothelium, nervous system, and the upper respiratory tract. Overall, this study identified cfRNA as a versatile analyte for the differential diagnosis and characterization of a wide range of pediatric inflammatory syndromes.

2024-09-11 | GSE255555 | GEO

Autoantibody Epitope Spreading in the Pre-Clinical Phase Predicts Progression to Rheumatoid Arthritis

Project description:This SuperSeries is composed of the following subset Series: GSE32016: Autoantibody Epitope Spreading in the Pre-Clinical Phase Predicts Progression to Rheumatoid Arthritis [ANALYTE: ANTIGEN] GSE32019: Autoantibody Epitope Spreading in the Pre-Clinical Phase Predicts Progression to Rheumatoid Arthritis [ANALYTE: Cytokine or chemokine] Refer to individual Series

2011-09-09 | E-GEOD-32021 | biostudies-arrayexpress

Absolute quantitation of proteins by two-point quantitation using dimethylated proteotypic peptides

Project description:Absolute targeted proteomics typically employs known amounts of synthetic stable isotopically labeled peptides which are mixed with the analyte and analysed by LC-MS. In order to obtain accurate data, we evaluated the use of two different stable isotopes of the same peptide as spike-in for absolute quantification. For this purpose, peptide labeling by reductive amination was applied, which is a mild reaction for dimethylation of amine groups with very high yield and very little side reactions. Furthermore, three different forms can be generated with e.g., light and heavy labels for spike-in peptides, and medium label for endogenous peptides. The addition of the dimethylated proteotypic peptide in two different versions allows to determine the accuracy of the quantification of endogenous peptides using the relative ratio of the intensities of the two internal standards. The method was studied with peptides of apolipoprotein A-I, apolipoprotein B-100, and leucine-rich alpha-2-glycoprotein without and with serum. In serum, the endogenous protein concentrations were accurately measured across four orders of magnitude by the two-point quantitation method. Less than 20% of coefficient of variation (CV) values and strong correlation with R2 of 0.99 across three analytical replicates was observed. The results showed that the accuracy to determine the amount of endogenous peptides can be validated using two references against each other, which cannot be obtained by one-point quantitation. Because of the significant lower costs than synthetic stable isotopically labeled peptides, this approach might be particularly interesting for the absolute quantitation of multiple proteins.

2018-11-27 | PXD007894 | Pride

AGATA: First nationwide molecular screening program in Spain for patients with advanced breast cancer

Project description:The SOLTI-1301 AGATA study aimed to assess the feasibility of a multi-institutional molecular screening program to better characterize the genomic landscape of advanced breast cancer (ABC) and to facilitate patient access to matched-targeted therapies in Spain. Between September 2014 and July 2017, 305 patients with ABC from 10 institutions were enrolled.

2021-11-01 | GSE182852 | GEO